title: The inactivation of enzymes belonging to the central carbon metabolism, a novel mechanism of developing antibiotic resistance

status: Public on May 11 2020

city: Cantoblanco

first: Juan

middle: Carlos

last: Oliveros

state: Madrid

address: Darwin 3

institute: CNB, CSIC

summary: Fosfomycin is a bactericidal antibiotic, analogous to phosphoenolpyruvate (PEP) that exerts its activity by inhibiting the activity of MurA. This enzyme catalyzes the first step of peptidoglycan biosynthesis, the transfer of enolpyruvate from PEP to uridine- diphosphate-N-acetylglucosamine. Fosfomycin is increasingly used in the last years, mainly for treating infections caused by Gram-negative multidrug resistant bacteria as Stenotrophomonas maltophilia, an opportunistic pathogen characterized by its low susceptibility to antibiotics of common use. The mechanisms of mutational resistance to fosfomycin in Stenotrophomonas maltophilia were studied in the current work. None of the mechanisms so far described for other organisms, which include the production of fosfomycin inactivating enzymes, target modification, induction of alternative peptidoglycan biosynthesis pathway and the impaired entrance of the antibiotic, are involved in the acquisition of such resistance by this bacterial species. Rather the unique cause of resistance in the studied mutants is the mutational inactivation of different enzymes belonging to the Embden-Meyerhof-Parnas central metabolism pathway. The amount of intracellular fosfomycin accumulation did not change in any of these mutants showing that neither the inactivation nor the transport of the antibiotic were involved. Transcriptomic analysis also showed that the mutants did not present changes in the expression level of putative alternative peptidoglycan biosynthesis pathway genes neither any related enzyme. Finally, the mutants did not present an increased PEP concentration that might compete with fosfomycin for its binding to MurA. Based on these results, we describe a completely novel mechanism of antibiotic resistance based on the remodeling of S. maltophilia metabolism.

overall_design: Stenotrophomonas maltophilia D457 and fosfomycin resistant mutants (FOS1, FOS4, FOS7 and FOS8)  mRNA profiles measured by paired-end RNA-seq

first: Teresa

last: Gil-Gil

first: Fernando

last: Corona

first: José

last: Martínez

first: Alejandra

last: Bernardini


title: Mutations in splicing factor SF3B1 promote transformation through MYC stabilization

status: Public on May 01 2020

city: NewYork

first: Zhaoqi

last: Liu

state: New York

address: ICRC Building 8th Floor, Office 803B 1130 St. Nicholas Ave

department: Systems Biology

country: USA

institute: Columbia university

type: Expression profiling by high throughput sequencing

summary: Although mutations in the RNA splicing factor SF3B1 are frequently observed in multiple human cancers, their functional role in promoting tumorigenesis and therapeutic significance remain poorly understood. Here we characterize the splicing landscape of 79 tumors and 12 isogenic cell lines harboring SF3B1 hotspot mutations, identifying hundreds of cryptic 3’ splice site (ss) events shared as well as specific to different tumor types. Regulatory network analysis shows that tumors harboring the most common hotspot mutation in SF3B1 (SF3B1K700E) activate the MYC transcriptional program. SF3B1 mutations lead to a dramatic decay of transcripts encoding the key PP2A phosphatase subunit PPP2R5A due to aberrant 3’ss usage, resulting in increased c-MYC serine 62 phosphorylation (allowing MYC to escape ubiquitin-mediated degradation) and in increased BCL2 serine 70 phosphorylation (leading to anti-apoptotic effects). This effect of SF3B1K700E on c-MYC and BCL2 activation through post-translational regulation was conserved across human and mouse cells and could be rescued by restored expression of PPP2R5A. Consonant with this, mutant SF3B1 promoted c-MYC driven tumorigenesis could be restored by the PP2A activating agent FTY-720. This study reveals the functional contribution of mutant SF3B1 to tumorigenesis through regulation of established oncogenic pathways and provides therapeutic strategies for related tumors.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: 16 samples, including 12 mouse and 4 human samples with varying SF3B1 status

first: Akihide

last: Yoshimi

first: Giulia

last: Fabbri


title: RNA Sequencing of C elegans wild type (N2) grown on 20 vs 5µg/ml cholesterol

status: Public on Apr 21 2020

city: Houston

first: Benson

last: Otarigho

state: Texas

address: 6767 Bertner Avenue

department: Department of Genetics

institute: The University of Texas MD Anderson Cancer Center

summary:
Purpose: Cholesterol is an essential nutrient for diverse biological processes in all organisms. However, the role of cholesterol in immune function remains understudied. Hence the goal is to obtain cholesterol-mediated immune genes
Methods: Hermaphrodite C. elegans (var. Bristol) wild type (N2) were grown on 20 along side with control, which is 5µg/ml cholesterol and harvested at L4 stage. Total RNA was extracted and RNA sequencing was done following standard protocols
Results: Detailed analyses of the transcriptomic data show that cholesterol-mediated immune gene that could enhance the fight against infectious diseases
Conclusions: This study showed a novel role for cholesterol in the enhancement of the innate

overall_design: C. elegans RNA seq of L4 grown on 20 and 5µg/ml cholesterol were generated by deep sequencing, in triplicate, using BGISEQ-500 platform

first: Alejandro

last: Aballay


title: CITEseq analysis of non-small-cell lung cancer lesions

status: Public on Jul 22 2020

city: NEW YORK

first: Miriam

last: Merad

address: 1470 Madison Ave, Room 5-301

department: Oncological Sciences

institute: ICAHN SCHOOL OF MEDICINE AT MOUNT SINAI

summary: Immunotherapy is becoming a mainstay in the treatment of NSCLC. We profiled immune cells of 35 early stage NSCLC lesions using multiscale single cell sequencing, including scRNAseq, CITEseq, and TCRseq.

overall_design: Samples of tumor and non-involved lung were obtained from surgical specimens of patients undergoing resection at Mount Sinai Hospital (New York, NY) after obtaining informed consent in accordance with a protocol reviewed and approved by the Institutional Review Board at the Icahn School of Medicine at Mount Sinai (IRB Human Subjects Electronic Research Applications 10-00472 and 10-00135) and in collaboration with the Biorepository and Department of Pathology. Tissues were rinsed in PBS, minced and incubated for 40 minutes at 37C in Collagenase IV 0.25mg/ml, Collagenase D 200U/ml and DNAse I 0.1mg.ml (all Sigma). Cell suspensions were then aspirated through a 18G needle ten times and strained through a 70-micron mesh prior to RBC lysis. Cell suspensions were enriched for CD45+ cells by either bead positive selection (Miltenyi) per kit instructions or FACS sorting on a BD FACSAria flow sorter. Cells were directly loaded onto a 10X Chromium single-cell encapsulation chip according to manufacturer instructions for scRNAseq, or were stained with CITEseq and hashing antibody panels prior to loading, then subjected to downstream encapsulation and respective library prep. Alternatively, cells were subject to CD2+ bead enrichment prior to encapsulation and joint TCR/gene expression RNAseq. Raw data files are uploaded on NCBI with SRA Study SRP251372 BioProject ID PRJNA609924

first: Andrew

middle: M

last: Leader

first: John

middle: A

last: Grout

first: Christie

last: Chang

first: Barbara

last: Maier

first: Alexandra

last: Tabachnikova

first: Laura

last: Walker

first: Alona

last: Lansky

first: Jessica

last: LeBerichel

first: Naussica

last: Malissen

first: Melanie

last: Davila

first: Jerome

last: Martin

first: Giuliana

last: Magri

first: Kevin

last: Tuballes

first: Zhen

last: Zhao

first: Francesca

last: Petralia

first: Robert

last: Samstein

first: Natalie

last: Roy D'Amore

first: Gavin

last: Thurston

first: Alice

last: Kamphorst

first: Andrea

last: Wolf

first: Raja

last: Flores

first: Pei

last: Wang

first: Mary

middle: B

last: Beasley

first: Helene

last: Salmon

first: Adeeb

middle: H

last: Rahman

first: Thomas

middle: U

last: Marron

first: Ephraim

last: Kenigsberg


title: Machine Learning Classification of Peripheral Blood Gene Expression Identifies at Baseline Subsets of Patients with Systemic Sclerosis Most Likely to Show Clinical Improvement in Response to Autologous Myeloablative Hematopoietic Stem Cell Transplantation

status: Public on Jul 01 2020

city: Lebanon

first: Tammara

last: Wood

state: NH

address: WTRB 674

department: Biomedical Data Science

institute: Dartmouth Medical School

summary: The SCOT (Scleroderma: Cyclophosphamide or Transplantation) trial demonstrated clinical benefit of autologous hematopoietic stem cell transplant (HSCT) compared to cyclophosphamide (CYC) in scleroderma. We analyzed gene expression from peripheral blood mononuclear cells (PBMCs) of SCOT participants to identify those with differential treatment response.

overall_design: PBMC gene expression data were generated from 63 SCOT participants at baseline and at follow-up timepoints. Participants who completed treatment protocol were stratified by intrinsic gene expression subsets at baseline, evaluated for event-free survival (EFS) and analyzed for differentially expressed genes.

first: Jennifer

last: Franks

first: Lynette

last: Keyes-Elstein

first: Peter

last: McSweeney

first: Viktor

last: Martyanov

first: Daniel

last: Furst

first: Richard

last: Nash

first: Ellen

last: Goldmuntz

first: Keith

last: Sullivan

first: Leslie

last: Crofford

first: Maureen

last: Mayes

first: Michael

middle: L

last: Whitfield


title: Resuscitated transcriptional network of a spurious transcription factor potentially facilitates transcriptional rewiring and adaptive evolution.

status: Public on Apr 08 2020

city: Taipei

first: Po-Chen

last: Hsu

address: 128 Academia Road, Section 2, Nankang

department: Institute of Molecular Biology

country: Taiwan

institute: Academia Sinica

type: Genome binding/occupancy profiling by high throughput sequencing

summary: We report the ChIP-seq profiling of a spurious transcriptional factor Sef1 in non-typical model yeast species, Lachancea kluyveri, and show that LkSef1 targets many TCA cycle and many others genes but has very limited regulatory effects to these target genes.

overall_design: LkSef1 ChIP-seq analysis was performed from three biological replicates of YPD- and YPGly-grown Sef1-TAP tagged cells, using Illumina NextSeq500 sequencer.

first: Jun-Yi

last: Leu


title: Inactivation of the nuclear interacting SET domain protein 1 (NSD1) impairs GATA1-regulated erythroid differentiation and causes erythroleukemia. NSD1 Add-back experiment, mRNASeq cultured erythroblasts.

status: Public on Apr 07 2020

city: Basel

first: DBM Bioinformatics

last: Core Facility

state: BS

address: Hebelstrasse 20

department: Departement of Biomedicine

country: Switzerland

institute: University of Basel

summary: In vitro differentiation of Nsd1-/- erythroblasts with retroviral expression of wildtype Nsd1, or a catalytically-inactive Nsd1N1918Q SET-domain

overall_design: Add-back experiment with cultured Nsd1-/- erythroblasts rescued with either retroviral expression of wildtype Nsd1, or a catalytically-inactive Nsd1N1918Q SET-domain

first: Katharina

last: Leonards

first: Marwa

last: Almosailleakh

first: Samantha

last: Tauchmann

first: Frederik

middle: O

last: Bagger

first: Robert

last: Ivanek

first: Juerg

last: Schwaller


title: Comparing the genome-wide chromatin accessibility of uhrf1 hi272 mutants and phenotypically wildtype whole zebrafish embryos at 120 hpf using ATAC-Seq.

status: Public on Jun 23 2020

city: Abu Dhabi

first: Kirsten

last: Sadler Edepli

state: Abu Dhabi

department: Biology

country: United Arab Emirates

institute: New York University Abu Dhabi

summary: The goal of this study is to study the chromatin accessibility differences between control and uhrf1 hi272 mutant 120 hpf zebrafish embryos (uhrf1 hi272+/-, Tg(fabp10a:CAAX-EGFP) using ATAC-Seq technique.

overall_design:
"Whole larvae (3 per genotype9 at 120 hpf from uhrf1-hi272 mutants and their pheotypically normal siblings were pooled, dissociated with trypsin and 50,000 live cells were used per library preparation.ATAC-seq: Protocol as described in Buenrostro et al (2015): doi:10.1002/0471142727.mb2129s109, using illumina barcoded primers for sequencing with the excpetion of dissociating the cells for cell suspension was obtained by treatment with trypsin at 37 degree for 30 minutes.
"

first: Bhavani

last: Madakashira

first: Chi

last: Zhang

middle: C

last: Sadler (Edepli)


title: The AAA+ ATPAse RUVBL2 is essential for the oncogenic function of c-MYB in acute myeloid leukemia

status: Public on Apr 14 2020

city: Nijmegen

first: Joost

last: Martens

state: Nederland

address: Geert Grooteplein 28

department: RIMLS

country: Netherlands

institute: Radboud University

summary: Subtype-specific leukemia oncogenes drive aberrant gene expression profiles that converge on common essential mediators to ensure leukemia self-renewal and inhibition of differentiation. The transcription factor c-MYB functions as one such mediator in a diverse range of leukemias. Here we show that transcriptional repression of myeloid differentiation associated c-MYB target genes in AML is enforced by the AAA+ ATPAse RUVBL2. Silencing RUVBL2 expression resulted in increased binding of c-MYB to these loci and their transcriptional derepression. RUVBL2 inhibition induced AML cell apoptosis and severely impaired disease progression of established AML in engrafted mice. In contrast, such inhibition had little impact on normal hematopoietic progenitor differentiation. These data reveal a central mechanism governing inhibition of myeloid differentiation by c-MYB in AML. They also indicate that targeting the control of c-MYB function by RUVBL2 is likely to be a promising approach to developing future anti-AML therapies.

overall_design: ChIP-seq using MYB and H3K27ac antibodies

first: Elena

last: Monterroso

first: Lu

last: Zhao

first: Luca

last: Gasparoli

first: Tony

last: Brooks

first: Kerra

last: Pearce

first: Marc

middle: R

last: Mansour

first: Jasper

last: de Boer

first: Owen

last: Williams


title: Lung-derived HMGB1 induces mitochondrial fission and impacts the proteolytic activity of arterial macrophages

status: Public on Aug 04 2020

city: New York

first: Bhama

last: Ramkhelawon

state: NY

address: 435 East 30th - Science Building 416

department: Surgery

institute: NYU Langone Medical Center

summary: This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: Regulatory divergence during limb evolution

status: Public on Mar 31 2020

first: DBM Bioinformatics

last: Core Facility

sample_organism:
Sus scrofa
Mus musculus

platform_organism:
Sus scrofa
Mus musculus


title: Regulatory divergence during pig limb evolution

summary: Genome-wide comparative analyses of the open chromatin profiles between equivalent stages of mouse and pig limb bud development reveal the extensive functional divergence of their limb regulomes. These alterations affect evolutionary conserved regions located in the genomic landscapes of genes with essential functions during limb development. This analysis uncovers the widespread regulatory changes that appear to underlie the morphological diversion of the artiodactyl limb from the pentadactyl blueprint of tetrapods.

overall_design: ATAC-seq analysis on dissected D21 and D24 pig forelimb buds

first: Javier

last: Lopez-Rios

first: Rolf

last: Zeller

first: Virginie

last: Tissieres

first: Florian

last: Geier


title: Regulation of Ag-activated B cells by Nur77/Nr4a1

status: Public on Mar 30 2020

city: San Francisco

first: Julie

last: Zikherman

state: CA

address: 513 Parnassus Ave, HSW1201a

institute: University of California San Francisco

summary: We identify differentially expressed inducible genes in activated B cells harvested from mice lacking expression of the orphan nuclear hormone receptor Nr4a1.

overall_design: Examination of RNA transcriptomes in both non-stimulated and stimulated B cells from wildtype and Nr4a1-/- mice, in order to identify differentially expressed inducible genes.

first: Corey

last: Tan

first: James

last: Mueller


title: Classification by a gene expression profile can help to select oxaliplatin- or irinotecan-based regimen for first-line treatment of metastatic colorectal cancer: Translational research of the TRICOLORE study

status: Public on Mar 27 2020

city: Sendai

first: Shin

last: Takahashi

address: 4-1, Seiryo-machi, Aobaku

department: Clinical Oncology

country: Japan

institute: Tohoku University

summary: The purpose of this study is to explore biomarkers related to clinical outcomes of OX and IRI as TR in the TRICOLORE trial, and a mutational analysis of colon-cancer-related genes, immunohistochemical staining, DNA methylation status, and a comprehensive gene expression analysis were performed as translational research (TR)

overall_design: Gene expression profile from 308 formalin-fixed and paraffin embedded primary tumor samples.

first: Kota

last: Ouchi

first: Akira

last: Okita

first: Keigo

last: Komine


title: ssDNA-seq mapping of DNA secondary structures in mouse ES cells

status: Public on Jun 29 2020

city: New Haven

first: Andrew

middle: Zhuo

last: Xiao

state: CT

address: 10 Amistad St

department: Genetics

institute: Yale Stem Cell Center

summary: DNA N6-methyladenine (N6-mA) is an emerging epigenetic mark in the mammalian genome. Levels of N6-mA undergo drastic fluctuation during early embryogenesis, indicative of active regulation. Here we demonstrate that the 2-oxoglurarate oxygenase ALKBH1 functions as a nuclear eraser of N6-mA in unpairing regions (e.g. SIDD, Stress Induced DNA Double Helix Destabilization regions). Enzymatic profiling studies revealed that ALKBH1 displays demethylation activity towards N6-mA on DNA substrates that share a common unpairing feature, e.g. bubbled, bulged or single-stranded DNA oligos. Furthermore, ssDNA-seq and DIP-seq analyses revealed significant genome-wide co-occurrence of base unpairing regions with N6-mA in mouse embryonic stem cells, especially during cell fate transition. Collectively, our biochemical, structural and genomic studies demonstrate that ALKBH1 is an important DNA demethylase that regulates genome N6-mA turnover in unpairing regions associated with dynamic chromatin regulation in early development.  This series contains data from ssDNA-seq experiments on mouse ES cells. We used the S1 nuclease and biotin end-labeling to enrich for DNA at ssDNA regions followed by HiSeq4000 sequencing and data analysis.

overall_design: Genomic DNA pulldown with HiSeq sequencing

first: Raman

middle: V

last: Nelakanti

middle: Z


title: Low input RNA sequencing of GPR35-positive and negative intestinal macrophages

status: Public on Jun 25 2020

summary:
Aim: We aimed to determine differences in transcriptional profiles of GPR35-positive and negative macrophages in the steady state intestine.
Method: Corresponding subpopulations were sorted by FACS from intestinal lamina propria cells of unmanipulated wild-type C56BL/6 mice. RNA from 4 replicates of each group were sequenced and analyzed.
Result: GPR35 positive macrophages are transcriptionally distinct from GPR35 negative macrophages overall with 2798 downregulated and 2773 upregulated genes, and regarding cytokine expression profile with higher Il1b, Tnf and Il10 mRNA expressions.
Conclusion: Our study reports the first analysis on transcriptional charasteristics of intestinal macrophages depending on their GPR35 expression providing insights into the function of GPR35 in these cells.

overall_design: mRNA profiles of GPR35- positive and negative macrophages in the colonic lamina propria

first: Kaya

last: Berna

first: Geier

last: Florian

first: Beisel

last: Christian


title: Global gene expression analysis of primary head and neck cancer cases

status: Public on Jun 19 2020

city: Heidelberg

first: Omics IT & Data Management

last: Core Facility

address: Im Neuenheimer Feld 280

department: Omics IT & Data Management Core Facility

country: Germany

institute: German Cancer Research Center (DKFZ)

summary: This study addressed the assumption that in addition to somatic mutations epigenetic silencing of cancer-related genes by promoter hyper-methylation is a common event in head and neck cancer. A multi-scale omics approach based on whole-exome sequencing, global DNA methylation and gene expression profiling data derived from tumor samples of the HIPO-HNC cohort was conducted and new findings were confirmed with data from TCGA-HNC. Results provide experimental evidence that the ryanodine receptor 2 (RYR2) exhibits variable promoter methylation and expression in both tumor samples and HNSCC cell lines. Moreover, immunohistochemical staining of tissue sections unraveled a gradual loss of RYR2 expression from normal mucosa via dysplastic lesions to cancer, and indicated that reduced RYR2 expression in adjacent tissue and precancer lesions might serve as a risk factor for unfavorable prognosis and upcoming malignant conversion.

overall_design: Total RNA obtained from primary head and neck cancer of the HIPO-HNC cohort

first: Karim

last: Zaoui

first: Jochen

last: Hess

first: Kolja

last: Freier

first: Wilko

last: Weichert

first: Roland

last: Eils

first: Xavier

last: Pastor Hostench


title: Ringsideroblasts in acute myeloid leukemia are associated with adverse risk and result from an abberant heme-metabolism gene program

status: Public on Mar 17 2020

first: Joost

last: Martens

summary: Ringsideroblasts(RS) emerge as result of aberrant erythroid differentiation leading to excessive mitochondrial iron accumulation. This feature is characteristic for myelodysplastic syndromes with mutations in spliceosome gene SF3B1. However, RS can also be observed in patients diagnosed with acute myeloid leukemia (AML). The objective of this study was to characterize the presence of RS in a cohort of 109 AML and 17 high-risk MDS patients. Clinically, RS-AML is enriched for ELN adverse-risk (55%). In line with this finding, 35% of all cases had complex cytogenetic aberrancies and TP53 was most recurrently mutated in this cohort (42%), followed by DNMT3A (29%), RUNX1 (21%) and ASXL1 (19%). In contrast to RS-MDS, the incidence of SF3B1 mutations was low (8%). Whole exome sequencing and SNP array analysis on a subset of patients did not uncover one single defect underlying the RS phenotype. Shared genetic defects between erythroblasts and total mononuclear cell fraction indicate common ancestry for the erythroid lineage and the myeloid blast cells in RS-AML patients. Gene expression analysis by performing RNA sequencing on CD34+ AML cells revealed differential gene expression between RS-AML and a separate AML cohort, including genes involved in megakaryocytic/erythroid differentiation and mRNA splicing. Furthermore, several heme-metabolism-related genes were found upregulated in RS-AML, as was observed in SF3B1mut MDS. These results demonstrate that erythroblasts share ancestry with malignant myeloid blast cells in RS-AML. The genetic background of RS-AML differs from that of RS-MDS, however downstream effector pathways may be comparable, providing a possible explanation for presence of RS in AML.

overall_design: RNA sequencing of primary AML samples containing Ringsideroblasts in bone-marrow smears

first: Gerbrig

last: Berger

first: Mylène

last: Gerritsen

first: Guoqiang

last: Yi

first: Edo

last: Vellenga


title: The repressive genome compartment is established early in the cell cycle before forming the lamina associated domains

city: Baltimore

first: Karen

last: Reddy

state: MD

address: 855 North Wolfe Street

department: Center for Epigenetics/Biological Chemistry

institute: Johns Hopkins University

summary: Three-dimensional (3D) genome organization is thought to be important for regulation of gene expression. Chromosome conformation capture-based studies have uncovered ensemble organizational principles such as active (A) and inactive (B) compartmentalization. In addition, large inactive regions of the genome associate with the nuclear lamina, the Lamina Associated Domains (LADs). Here we investigate the dynamic relationship between A/B-compartment organization and the 3D organization of LADs. Using refined algorithms to identify active (A) and inactive (B) compartments from Hi-C data and to define LADs from DamID, we confirm that the LADs correspond to the B-compartment. Using specialized chromosome conformation paints, we show that LAD and A/B-compartment organization are dependent upon chromatin state and A-type lamins. By integrating single-cell Hi-C data with live cell imaging and chromosome conformation paints, we demonstrate that self-organization of the B-compartment within a chromosome is an early event post-mitosis and occurs prior to organization of these domains to the nuclear lamina.

overall_design: DamID-seq in primary MEFs, and primary MEFs after epigenetic perturbation or laminA/C knockdown.

first: Teresa

last: Luperchio

first: Michael

middle: E

last: Sauria


title: Gene expression changes following dihydrotestosterone (DHT) treatment in HCI-009 PDXs

status: Public on Jun 11 2020

city: Aurora

first: Jessica

last: Christenson

state: CO

department: Pathology

institute: University of Colorado Anschutz Medical Campus

summary: Triple-negative breast cancer (TNBC) is aggressive and difficult, and few targeted therapies are available to treat this patient population. The androgen receptor (AR) has emerged as a potential target in breast cancer. Newer generation AR inhibitors, such as Seviteronel (Sevi), are unique in their ability to inhibit AR both directly and by blocking upstream androgen synthesis. The purpose of this study was to investigate the pre-clinical activity of Sevi in TNBC and further explore the effectiveness of targeting both androgen biosynthesis and AR activity in combination with other downstream acting agents. AR overexpressing (AR+) TNBC cell lines, xenografts and androgen responsive patient-derived xenograft (PDX) models were using to show how effectively Sevi inhibits AR activity and cell/tumor proliferation. Single cell RNA-sequencing of the AR+ cell line MDA-MB-453 illustrated heterogeneity in AR levels and identified cell cycle pathway activation in ARHigh versus ARLow expressing cells. Combination treatment with the cell cycle CDK4/6 inhibitor abemaciclib and Sevi showed synergy in AR+ TNBC cells and increased effectiveness, compared to each drug alone, in an AR+ TNBC xenograft model. While cell cycle inhibitors have been approved for use in hormone-receptor positive breast cancer, our studies suggest that these drugs may be equally effective in AR+ TNBC cells, especially when combined with AR antagonists.    Implications. These data suggest that targeting AR signaling at multiple points throughout the pathway may be an effective was to treat patients with AR+ TNBC.

overall_design: HCI-009 is a TNBC PDX originally developed in the laboratory of Dr. Alana Whelm and propagated in immunodeficient NOD/SCID/gamma (NSG) mice. In the DHT experiment (n=3-4 mice per group), cycling female NSG mice were implanted with cellulose control or slow release 8mg DHT pellets.  PDX tumor portions were bilaterally, orthotopically injected into the mammary fat pads, and tumors were measured weekly by caliper for 9 weeks.

first: Kathleen

middle: I

last: O'Neill

first: Michelle

last: Williams

first: Nicole

last: Spoelstra

first: Kenneth

last: Jones

first: G

middle: D

last: Trahan

first: Elaina

last: Van Patten

first: Joel

last: Eisner

first: Jennifer

middle: K

last: Richer


title: Transcriptomic profiling of Cu-regulated genes in an oceanic diatom

status: Public on Feb 29 2020

city: Montreal

first: Liangliang

last: Kong

state: Quebec

address: 1205 Docteur Penfield

country: Canada

institute: McGill

summary: Copper (Cu) plays an essential role in cellular metabolism and limits phytoplankton growth and production in parts of the open sea. Whole transcriptome analysis provides a powerful tool to explore gene expression profiles and cellular metabolic pathways regulated by Cu.  In this study, we identified Cu-regulated genes by profiling the transcriptomes of an oceanic diatom, Thalassiosira oceanica 1005, adapted to survive in a Cu-limited and Cu-replete environment. The results provide insights to the mechanisms of adaptation and acclimation of T. oceanica to low Cu environments.

overall_design: Examination of Cu-replete, Cu-limited and Cu-transient cells, in triplicate, using Illumina Hiseq 2000

first: Neil

last: Price


title: CD34+ AML cells with low mitochondrial activity show increased expression of stemness-genes and can be targeted by the BCL-2 inhibitor Venetoclax

status: Public on May 24 2020

first: Joost

last: Martens

summary: It has been shown that AML cells with low levels of reactive oxygen species (ROS) have characteristics of LSCs as defined by in vitro and in vivo experiments. We investigated how distinct ROS levels within the stem cell enriched AML CD34+ cell fraction correlate with cellular functions and characteristics such as morphology, metabolic activity, gene expression and drug responsiveness. The results demonstrate that CD34+ AML cells with low ROS levels corresponded with the CD34+/CD38- AML subfraction and showed significantly increased expression of stemness-associated genes and negative regulators of signaling and had a lower mitochondrial number and activity. Moreover, CD34+ AML cells with low ROS levels could be efficiently targeted with the BCL-2 inhibitor Venetoclax despite their similar BCL-2 expression levels compared to the less sensitive CD34+ AML fraction with high ROS levels.

overall_design: RNA sequencing of primary AML samples sorted for ROSlow and ROShigh

first: Katherina

last: Mattes

first: Mylene

last: Gerritsen


title: Rewiring of gene expression in PWBC at artificial insemination is predictive of pregnancy outcome in cattle (Bos taurus)

status: Public on Feb 28 2020

city: Blacksburg

first: Fernando

last: Biase

state: VA

address: 175 West Campus Drive

department: School of Animal Sciences

institute: Virginia Tech

summary: Infertility is a disease that affects humans and cattle in similar ways. The resemblance includes complex genetic architecture, multiple etiology, low heritability of fertility related traits in females, and the frequency in the female population. Here, we used cattle as a biomedical model to test the hypothesis that gene expression profiles of protein-coding genes expressed in peripheral white blood cells (PWBCs), and circulating micro RNAs in plasma, are associated with female fertility, measured by pregnancy outcome. We drew blood samples from 17 female calves on the day of artificial insemination and analyzed transcript abundance for 10496 genes in PWBCs and 290 circulating micro RNAs. The females were later classified as pregnant to artificial insemination, pregnant to natural breeding or not pregnant. We identified 1860 genes producing significant differential coexpression (eFDR<0.002) based on pregnancy outcome. Additionally, 237 micro RNAs and 2274 genes in PWBCs presented differential coexpression based on pregnancy outcome. Furthermore, using a machine learning prediction algorithm we detected a subset of genes whose abundance could be used for blind categorization of pregnancy outcome. Our results provide strong evidence that bloodborne transcript abundance is highly associated with fertility in females.

overall_design: 17 heifers classified as not-pregnant (n=5), AI-pregnant (n=6) and NB-pregnant (n=6)

first: Sarah

last: Moorey


title: RNA sequencing of NCR- ILC3s

status: Public on Mar 16 2020

first: DBM Bioinformatics

last: Core Facility


title: Gene expression of RAW264.7 with or without Pdpn expression before and after H. pylori infection

status: Public on May 28 2020

city: Kuala Lumpur

first: Won

middle: Fen

last: Wong

address: Lembah Pantai

department: Department of Medical Microbiology,  Faculty of Medicine

country: Malaysia

institute: University of Malaya

summary: The effect of Podoplanin (Pdpn) expression on the differential expression profile of RAW264.7 cells has been characterised in wildtype, Pdpn knockout cells and Pdpn overexpressed cells before and after H. pylori infection using 770 genes from the NanoString Mouse PanCancer Pathways Panel.

overall_design: Three models of RAW264.7 cell lines including wildtype, Pdpn knockout and Pdpn overexpressed were seeded and infected with H. pylori SS1 strain at MOI 10:1 for 24 hours. PBS was used as mock infection and experiement were carried out with biological duplicates. RNA were harvested from all 12 samples, quantified and subjected to NanoString mouse PanCancer Pathways Panel with 770 genes.

first: Yi

middle: Y

last: Cheok

middle: F


title: Characterization of Aspergillus fumigatus NsdC transcription factor (RNA polII ChIP-seq)

status: Public on May 14 2020

city: Ribeirao Preto

first: Gustavo

middle: Henrique

last: Goldman

state: Sao Paulo

address: Avenida do Cafe

country: Brazil

institute: Sao Paulo University

summary: We use ChIP-seq technique to access RNA polymerase II enrichment in wild type and nsdC A. fumigatus null mutant before and after calcium exposure

overall_design: Examination of transcriptional changes after calcium exposure in A. fumigatus wild type and nsdC null mutant

first: Ana

last: Colabardini

first: Patricia

middle: A

last: de Castro


title: OXPHOS bioenergetic compensation does not explain disease penetrance in Leber hereditary optic neuropathy

status: Public on Feb 08 2020

city: Melbourne

first: Mark

last: Ziemann

state: VIC

address: 85 Commercial Rd

department: Bioinformatics Working Group

country: Australia

institute: Burnet Institute

summary: Leber hereditary optic neuropathy (LHON) is one of the most common primary mitochondrial diseases. It is caused by point mutations in mitochondrial DNA (mtDNA) genes and in some cases, it can result in irreversible vision loss, primarily in young men. It is currently unknown why LHON mutations affect only some carriers and whether bioenergetic compensation enables asymptomatic carriers to overcome mitochondrial impairment and preserve cellular function. Here, we conducted bioenergetic metabolic assays and RNA sequencing to address this question using male-only, age-matched, m.11778G>A lymphoblasts and primary fibroblasts from both carriers and affected individuals.  Our work indicates that OXPHOS bioenergetic compensation in LHON peripheral cells does not explain disease phenotype. We show that complex I impairment is similar in carrier and affected cells, despite a transcriptional downregulation of metabolic pathways including glycolysis in affected cells relative to carriers detected by RNA sequencing. Although we did not detect OXPHOS bioenergetic compensation in carrier cells, our results indicate that affected cells suffer a growth impairment under metabolic challenge compared to carrier cells, which were unaffected by metabolic challenge. If recapitulated in retinal ganglion cells, decreased susceptibility to metabolic challenge in carriers may help preserve metabolic homeostasis in the face of the mitochondrial complex I bioenergetic defect.

overall_design: The m.11778G>A mitochondrial polymorphism contributes to the development of LHON, but the majority of individuals with the mutation do not develop LHON. We obtained fibroblasts from individuals with LHON (n=3 affected), individuals with the polymorphism but no signs of LHON (n=3 carriers), and individuals without the polymorphism. Fibroblasts underwent RNA-seq.

first: M

middle: G

last: Lopez Sanchez

first: Nicole

middle: J

last: Van Bergen

first: Lisa

middle: S

last: Kearns

first: Helena

last: Liang

first: Alex

middle: W

last: Hewitt

first: David

last: Mackey

first: Ian

last: Trounce


title: Genetic ablation of either G6P-isomerase or dual LDHA/B in colon cancer cells LS174T , +/- MPP+ (1-methyl-4-phenylpyridinium)

status: Public on Apr 25 2020

city: Tallahassee

first: Elizabeth

last: Mazzio

state: Florida

address: 1515 MLK Blvd

department: College of Pharmacy & Pharmaceutical Science

institute: Florida Agricultural & Mechanical University

summary: In this study we explore the genomic re-wiring of a human colon cancer cell line (LS174T) in which fermentative glycolysis has been fully suppressed by CRISPR/Cas9 to disrupt glucose-6-phosphate isomerase (GPI-KO) or dual disruption of lactate dehydrogenases A and B (LDHAB-DKO). The effects of both KOs, had no effect on loss of viable cell function, corresponding to high concentrations of ATP production vs WT. All three clones were evaluated for  transcriptomic changes using GeneChip™ Human Gene 2.1 ST Arrays by Affymetrix Inc assessing for mRNAs and long intergenic non-coding RNA transcripts.

overall_design:
Six conditions:
LS174T Colon Cancer Vector Control
LS174T Colon Cancer LDHAB Double Knock Out
LS174T Colon Cancer G6PI Knock Out
LS174T Colon Cancer Vector Control + MPP+
LS174T Colon Cancer LDHAB Double Knock Out + MPP+
LS174T Colon Cancer G6PI Knock Out + MPP+

first: E

first: K

last: Soliman

first: S

last: Cassim

last: Zdralevic

first: J

last: Pouyssegur

first: N

last: Mack


title: RNA sequencing analysis of monocrotaline-induced pulmonary arterial hypertension

status: Public on May 02 2020

city: Fuzhou

first: Genfa

last: Xiao

state: Fujian

address: chazhong road 20

country: China

institute: First Affiliated Hospital of Fujian Medical University

summary: Inflammation and immunity play a causal role in the pathogenesis of pulmonary vascular remodeling and pulmonary arterial hypertension (PAH). However, the pathways and mechanisms by which inflammation and immunity contribute to pulmonary vascular remodeling remain unknown. RNA sequencing was used to analyze the transcriptome in control and rats injected with monocrotaline (MCT) for 1, 2, 3 and 4 weeks. Using the transcriptional profiling of MCT-induced PAH coupled with bioinformatics analysis, we clustered the differentially expressed genes (DEGs) and chose the increased expression patterns associated with inflammatory and immune response. We found the enrichment of Toll-like receptor (TLR) and NOD-like receptor (NLR) pathways and identified NF-κB-mediated inflammatory and immune profiling in MCT-induced PAH. Pathway-based data integration and visualization showed the dysregulated TLR and NLR pathways, including increased expression of TLR2 and NLRP3, and their downstream molecules. Further analysis revealed that the activation of TLR and NLR pathways was associated with upregulation of damage-associated molecular patterns (DAMPs) and RIPK3-mediated necroptosis was involved in the generation of DAMPs in MCT-induced PAH. Collectively, we identify RIPK3-mediated necroptosis and its triggered TLR and NLR pathways in the progression of pulmonary vascular remodeling, thus, providing novel insights into the mechanisms underlying inflammation and immunity in the pathogenesis of PAH.

overall_design: Lung transcriptional profiling of control and rats injected with monocrotaline (MCT) for 1, 2, 3 and 4 weeks was generated by the high-throughput RNA sequencing using Illumina 2000, n=5 control and n=3 for each MCT treatment week.

first: Liangdi

last: Xie


title: Effect of Chronic Ethanol Consumption in Rhesus Macaques on the Nucleus Accumbens Core Transcriptome

status: Public on Feb 06 2020

city: Portland

first: Priscila

last: Darakjian

state: OR

address: 3181 SW Sam Jackson Park Road, L470

department: Behavioral Neuroscience

institute: Oregon Health and Science University

summary: The current study was undertaken to expand on observations that transcriptome changes identified in the NAcc of Rhesus macaques underlies excessive ethanol consumption. Genome-wide RNA-Seq was used to examine the NAcc transcriptome in control, low/binge drinking and heavy/very heavy drinking animals. One key goal of the study was to determine if, as predicted and suggested by the epigenetic studies, excessive chronic ethanol consumption involves genes enriched in annotations associated with synaptic plasticity and specifically glutamate and GABA signaling plasticity.

overall_design: NAcc samples were obtained from four cohorts (cohorts 4, 5, 7a and 7b) of unrelated adult, male rhesus macaques (Macaca mulatta).Monkeys were trained to use operant drinking panels to obtain all fluids (water and/or ethanol) and meals. Once trained, they underwent four months of schedule-induced polydipsia (SIP) to induce ethanol self-administration in daily sessions (Grant et al., 2008). Control subjects were housed in the same room as the ethanol drinking subjects of the same cohort and participated in all experimental manipulations. For the controls, SIP and self-administration conditions were identical, with the exception that both spouts dispensed water. Libraries without strand orientation were prepared using the TruSeq RNA Sample Preparation Kit version 2 (Illumina). Libraries were sequenced according to specification on a HiSeq 2500 (Illumina) at the Oregon Health and Science University Massively Parallel Sequencing Shared Resource. PolyA-selected libraries were multiplexed three per lane, yielding an average of 76 million total single-end reads per sample. FastQC (Babraham Bioinformatics) was used for quality checks on the raw sequence data. Reads were aligned to MacaM genome assembly  using STAR version 2.5.2b (Dobin et al., 2013) with default parameters except for the following: outFilterMismatchNmax = 2 and outFilterMultimapNmax = 1. Using HTSeq version 0.6.1p1 (Anders et al., 2015) and the MacaM_Rhesus_Genome_Annotation_v7.8.1 GTF annotation file read counts were summarized at the gene level. On average, 70% of reads uniquely mapped to the MacaM genome. Generalized linear models, using DESeq2 (Love et al., 2014), were used to detect differential expression between High Drinkers and Controls (HDvsControls), Low Drinkers and Controls (LDvsControl), and High Drinkers and Low Drinkers (HDvsLD).

last: Walter

first: Robert

last: Hitzemann

first: Katherine

last: Grant

first: Christina

last: Zheng

first: Rita

last: Cervera-Juanes

first: Verginia

last: Cuzon-Carlson

first: Denesa

last: Lockwood

last: Searles


title: RNA Sequencing of C elegans wild type (N2) grown on 0µg/ml relative to animal grown 5µg/ml cholesterol

status: Public on Apr 21 2020

city: Houston

first: Benson

last: Otarigho

state: Texas

address: 6767 Bertner Avenue

department: Department of Genetics

institute: The University of Texas MD Anderson Cancer Center

summary:
Purpose: Cholesterol is an essential nutrient for diverse biological processes in all organisms. However, the role of cholesterol in immune function remains understudied. Hence the goal is to obtain cholesterol-mediated immune genes
Methods: Hermaphrodite C. elegans (var. Bristol) wild type (N2) were grown on 0µg/ml along side with control, which is 5µg/ml cholesterol and harvested at L4 stage. Total RNA was extracted and RNA sequencing was done following standard protocols
Results:  Detailed analyses of the transcriptomic data show that cholesterol-mediated immune gene that could enhance the fight against infectious diseases
Conclusions: This study showed a novel role for cholesterol in the enhancement of the innate

overall_design: RNA seq  profiles of L4-stage and wild type (WT) C elegans animals were generated by deep sequencing, using BGISEQ-500 platform.

first: Alejandro

last: Aballay


title: Multiple sclerosis cortical normal-appearing grey matter, grey matter lesions, and control grey matter

status: Public on Jan 13 2020

city: Basel

first: DBM Bioinformatics

last: Core Facility

address: Hebelstrasse 20

institute: University of Basel

summary: This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: CBFβ-SMMHC affects genome-wide Polycomb Repressive Complex 1 activity in Acute Myeloid Leukemia

status: Public on Jan 22 2020

city: Nijmegen

first: Joost

last: Martens

address: Geert Grooteplein 28

institute: Radboud University

summary: Polycomb activity is frequently altered in acute leukaemia through mutation or deletion of Polycomb Repressive Complex (PRC) components. Alterations in PRC-interacting factors such as the Core Binding Factor (CBF) complex should also affect leukemia biology, even if PRC composition is normal. We report that the acute myeloid leukemia (AML)-associated CBFβ-SMMHC fusion oncoprotein physically interacts with the PRC1 complex, and that these factors co-localize across the AML genome in a PRC2-independent manner. Depletion of CBFβ-SMMHC caused increases in genome-wide PRC1 binding and an altered association between PRC1 and RUNX1. Overall, PRC1 was more likely to be associated with active genes. CBFβ-SMMHC depletion had variable transcriptional effects, including significant reductions in expression of PRC1-bound ribosomal loci. Our results expand on the recently reported localized effect of CBFβ-SMMHC on RUNX1-mediated recruitment of PRC1 at MYC enhancer elements, providing evidence that the oncoprotein diversely affects Polycomb recruitment and transcriptional regulation across the entire AML genome.

overall_design: ChIP-seq and RNA-seq using an AML cell line harbouring a dox inducible CBFB-MYH11 knockdown construct (induction using 600 ng/ml dox for 72 hours) plus ChIP-seq of engrafted primary inv(16) AMLs

first: Gaelle

last: Cordonnier

first: Amit

last: Mandoli

first: Nicolas

last: Cagnard

first: Guillaume

last: Hypolite

first: Laura

last: Jussen

first: Ludovic

last: Lhermitte

first: Els

last: Verhoeyen

first: Vahid

last: Asnafi

first: Niall

last: Dillon

first: Elizabeth

last: Macintyre

first: Jonathan

last: Bond


title: The acute myeloid leukemia associated AML1-ETO fusion protein alters the transcriptome and cellular progression in a single-oncogene expressing in vitro induced pluripotent stem cell based granulocyte differentiation model

status: Public on Jan 14 2020

summary: Here we describe the development and characterization of an induced pluripotent stem cell (iPSC) system that allows in vitro differentiation towards different mature myeloid cell types such as monocytes and granulocytes. During in vitro differentiation we inducible expressed the AML1-ETO fusion protein and examined the effects of the oncoprotein on differentiation and the underlying alterations in the gene program. Our analysis revealed that AML1-ETO as a single oncogenic hit in a presumable non-mutated background blocks granulocytic differentiation and deregulates the gene program via altering the acetylome of the differentiating granulocytic cells and inducing t(8;21) AML associated leukemic characteristics.

overall_design: Transcriptome analysis and H3K27ac ChIP-seq of control and AML1-ETO induced iPSCs was performed using illumina high-throughput sequencing

first: Esther

last: Tijchon

first: Gouqiang

last: Yi

first: Jos

last: Smits

first: Francesco

last: Ferrari

first: Falco

last: Wijnen

first: Bowon

last: Kim

first: Eva

middle: M

last: Janssen-Megens

first: Jan

last: Schuringa

middle: H


title: Inactivation of the nuclear interacting SET domain protein 1 (NSD1) impairs GATA1-regulated erythroid differentiation and causes erythroleukemia.

status: Public on Apr 07 2020

first: DBM Bioinformatics

last: Core Facility


title: Multiple sclerosis cortical normal-appearing grey matter and control grey matter

summary: Multiple sclerosis (MS) is a chronic inflammatory demyelinating disease of the brain. Among characteristics of MS pathology are cortical grey matter abnormalities, which have been linked to clinical signs such as cognitive impairment. To understand MS cortical grey matter pathogenesis, we performed differential gene expression analysis of MS normal appearing grey matter (NAGM) and control grey matter. HLA-DRB1 is the transcript with highest expression in MS NAGM with a bimodal distribution among the examined cases. Genotyping revealed that every case with the MS-associated HLA-DR15 haplotype also shows high HLA-DRB1 expression. Quantitative immunohistochemical analysis confirmed the higher expression of HLA-DRB1 in HLA-DRB1*15:01 cases at the protein level. Analysis of grey matter lesion size revealed a significant increase of cortical lesion size in cases with high HLA-DRB1 expression. Our data indicate that increased HLA-DRB1 expression in the brain of MS patients may be an important factor in how the HLA-DR15 haplotype contributes to MS risk in the target organ.

overall_design: MS- and control tissue samples were provided by the UK Multiple Sclerosis Tissue Bank (UK Multicentre Research Ethics Committee, MREC/02/2/39). In total, 42 tissue samples from 14 control as well as 64 tissue samples from 25 MS cases were used for the gene expression analysis between NAGM and control GM.

first: L

last: Enz

first: T

last: Zeis

first: F

last: Geier

first: D

last: Schmid

first: G

last: Steiner

first: U

last: Certa

first: N

last: Schaeren-Wiemers


title: Inactivation of the nuclear interacting SET domain protein 1 (NSD1) impairs GATA1-regulated erythroid differentiation and causes erythroleukemia. KO experiement, mRNASeq whole bone-marrow.

summary: Bone marrow of lin-neg erythroblasts either diseased Nsd1-/- or healthy Nsd1fl/fl

overall_design: Knockout vs. wt NSD1

first: Katharina

last: Leonards

first: Marwa

last: Almosailleakh

first: Samantha

last: Tauchmann

first: Frederik

middle: O

last: Bagger

first: Robert

last: Ivanek

first: Juerg

last: Schwaller


title: Regulatory divergence during mouse limb evolution

status: Public on Mar 31 2020

summary: Genome-wide comparative analyses of the open chromatin profiles between equivalent stages of mouse and pig limb bud development reveal the extensive functional divergence of their limb regulomes. These alterations affect evolutionary conserved regions located in the genomic landscapes of genes with essential functions during limb development. This analysis uncovers the widespread regulatory changes that appear to underlie the morphological diversion of the artiodactyl limb from the pentadactyl blueprint of tetrapods.

overall_design: ATAC-seq analysis on dissected E10.5 and E11.5 mouse forelimb buds

first: Javier

last: Lopez-Rios

first: Rolf

last: Zeller

first: Virginie

last: Tissieres

first: Florian


title: DNA methylation profiles in Taiwanese patients of Type-2 Diabetes (T2D) associated to Nephropathy (DN) and Retinopathy (DR)

status: Public on Jan 07 2020

city: Taichung

first: Fuu-Jen

last: Tsai

address: No.2, Yude Rd., North Dist.

department: Department of Medical Research

institute: China Medical University Hospital

type: Methylation profiling by genome tiling array

summary:
There are the differential levels of methylation in the groups with and without complication to its control groups as non-diabetes and T2D without complication, two of which were classified into male and female, affects strictly the gene regulation to diabetic pathogenesis.
To screen specific candidates for detecting classification of Type-2 Diabetes without or with retinopathy or nephropathy, the level of DNA methylation is the one of considerable factors to influence the differential gene expression was inspected involvement of chromosome modification. The information of homeostasis inside nucleus causes highly conserved control to gene regulation, which leads to chronic disease as Type-2 Diabetes to its complication.

overall_design: The blood samples were collected individually from the volunteer participants, were diagnosed to assign groups as non-diabetes, diabetes without complication, diabetes with proliferative retinopathic complication, diabetes with non-proliferative retinopathic complication and diabetes with nephropathic complication. The whole blood of individual sample was processed and analyzed with Human Promoter 1.0R Array by following the instructed protocol of Affymetrix company.

first: Thai

middle: Q

last: Tran

first: Shih

last: Chen

first: Fuu


title: Comparison of transcriptional profiles of cultured intestinal ILC3s to freshly isolated splenic and intestinal ILC3s

status: Public on Mar 17 2020

first: DBM Bioinformatics

last: Core Facility

summary: ILC3s from the spleen (SP) and small intestine (SI) have been shown to be phenotypically and functional different. Intestinal factors are likely to regulate transcriptional profiles and thereby function of ILC3s. The goal of this study is to analyze if SI ILC3s acquire a SP-similar transcriptional profile after in vitro culture. Therefore transcriptional profiles of cultured SI ILC3s were compared to freshly isolated ILC3s of the murine SP and the SI by RNA seq technology. Cell suspension were generated from both organs and ILC3s (CD117+, Thy1.2+, KLRG1-, lin- (CD3, CD8, CD11b, CD11c, CD19, B220, Gr-1, TCRβ, TCRγδ, TER-119, NK1.1)) were sort purified. SI ILC3 were cultured for 7 days in vitro with IL-2, IL-7 and SCF. RNA was isolated and RNA sequencing was done using Ilumina Hiseq 2500 system and NuGEN Ovation RNA Seq System V2, with biological replicates. We show that intestinal ILC3 acquire a splenic-similar transcriptional profile after in vitro culture.

overall_design: RNA sequencing of ILC3 was done using Ilumina Hiseq 2500 system and NuGEN Ovation RNA Seq System V2, with biological replicates

first: Frank

last: Lehmann

first: Daniela

last: Finke


title: Identification of predictive markers for human mesenchymal stromal cells chondrogenic potential is challenged by donor variability

summary: Human bone marrow derived mesenchymal stromal cells (BMSCs) represent a putative cell source candidate for tissue engineering based strategies to repair cartilage and bone. However, traditional isolation of BMSCs by their preference to adhere to plastic leads to very heterogeneous cell populations and may account for high inter-donor variability and unpredictability of chondrogenic differentiation out-come. Identification of a cell fraction with higher chondrogenic capacity and reduced variance in basic chondrogenic differentiation could further aid the process for developing BMSC-based cartilage and bone regeneration approaches. Since single cell derived clones isolated from fresh bone marrow aspirates show a broad range of chondrogenic capacity, we assessed whether the gene expression profile of clones with high and low chondrogenic capacity differs. While a clustering between high and low chondrogenic capacity clones was observed for one donor, donor-to-donor variability drastically hampered the possibility to achieve conclusive results when different donors were considered. NCAM1/CD56 as identified by the transcriptomic analysis of one donor was still up-regulated in clones with higher chondrogenic capacity and we showed that enriching expanded multiclonal BMSCs for CD56+ expression led to an increase in chondrogenic capacity, though still highly affected by donor-to-donor variability. Our study finally suggests that the definition of predictive marker(s) for BMSCs chondrogenesis is challenged by the high donor’s heterogeneity of these cells. Moreover, we hypothesis that multiple pathways may be involved in determining the chondrogenic potential of BMSCs, making the identification of putative markers still an open issue.

overall_design: 34 single cell derived clones from 4 different donors

first: Chiara

last: Stüdle

first: Paola

last: Occhetta

last: Geier

first: Arne

last: Mehrkens

first: Andrea

last: Barbero

first: Ivan

last: Martin


title: HNF4α Pathway Mapping Identifies Wild-type IDH1 as a Targetable Metabolic Node in Gastric Cancer

status: Public on Jan 01 2020

city: Singapore

first: Wen Fong

last: Ooi

address: 60 Biopolis

country: Singapore

institute: Genome Institute of Singapore

summary: Comprehensive downstream mapping of HNF4α revealed its role in regulating GC metabolism via regulation of IDH1

overall_design: HNF4α ChIP-seq of GC cell lines, RNA-seq data of HNF4α perturbation and transcritome primary GC dataset were integrated to reveal HNF4α regulating biological processes and targets in GC, thus provide new therapeutic opportunity.

first: Chang

last: Xu

first: Ooi

last: Fong

first: Patrick

last: Tan


title: Bulk RNA sequencing of NCR- ILC3s from the murine spleen and the small intestine

summary: Splenic and intestinal NCR- ILC3s have been shown to be phenotypically and functional different. The goal of this study is to compare transcriptional profiles of NCR- ILC3s isolated of the murine spleen (SP) and the small intestine (SI) by RNA seq technology. Cell suspension were generated from both organs and NCR- ILC3s (CD117+, Thy1.2+, eYFP+, lin- (CD3, CD8, CD11b, CD11c, CD19, B220, Gr-1, TCRβ, TCRγδ, TER-119, NK1.1, NKp46)) were sort purified. RNA was isolated and RNA sequencing was done using Ilumina Hiseq 2500 system and NuGEN Ovation RNA Seq System V2, with biological triplicates. We provide the first comparison of transcriptional profiles of intestinal and splenic NCR- ILC3s.

overall_design: RNA sequencing of ILC3 was done using Ilumina Hiseq 2500 system and NuGEN Ovation RNA Seq System V2, with biological triplicates

first: Robert

last: Ivanek


title: Gender specific transcription regulation in the prefrontal cortex following social defeat stress

status: Public on Mar 12 2020

city: New York City

first: Jun

last: Wang

address: 1 Gustave L. Levy Pl, New York

department: Neurology

institute: Icahn School of Medicine at Mount Sinai

summary: Major depressive disorder (MDD) affects ~20% of the world population and is characterized by strong sexual dimorphism with females being 2-3 times more likely to develop this disorder. Previously, we demonstrated that a combination therapy with dihydrocaffeic acid (DHCA) and malvidin-glucoside (Mal-gluc) to synergistically target peripheral inflammation and stress-induced synaptic maladaptation in the brain was effective in alleviating chronic social defeat stress (CSDS)-induced depression-like phenotype in male mice. Here, we test the combination therapy in a female CSDS model for depression and compared sex-specific responses to stress in the periphery and the central nervous system. Similar to male mice, the combination treatment is also effective in promoting resilience against the CSDS-induced depression-like behavior in female mice. However, there are sex-specific differences in peripheral immune responses and differential gene regulation in the prefrontal cortex to chronic stress and to the treatment. These data indicate that while therapeutic approaches to combat stress-related disorders may be effective in both sexes, the mechanisms underlying these effects differ, emphasizing the need for inclusion of both sexes in preclinical studies using animal models.

overall_design:
We report gender specific transcriptome regulation in the prefrontal cortex in mice following social defeat stress and the effect of dihydrocaffeic acid and malvidin-glucoside treatment
Prefrontal cortex total RNA was isolated from stressed, non-stressed and stressed with treatment male and female mice and subjected to RNA-seq analysis

first: Ke

last: Hao


title: Transcriptome of new DROSHA_KO mouse embryonic stem cells generated by paired CRISPR/Cas9 approach

city: Zurich

first: Constance

last: Ciaudo

email: cciaudo@ethz.ch, ciaudobeyer@gmail.com

address: Otto-Stern-Weg 7

department: D-BIOL

institute: ETH

summary: Purpose:  The goals of this study was to obtain the trasncriptome of DROSHA_KO mESCs to compare it with the transcriptome of WT mESCs (deposit separately).

overall_design: mRNA profiles of DROSHA_KO mouse embryonic stem cells were generated by deep sequencing, in duplicate, using Illumina HiSeq2000.


title: Inactivation of the nuclear interacting SET domain protein 1 (NSD1) impairs GATA1-regulated erythroid differentiation and causes erythroleukemia. NSD1 Add-back experiment. ChIPSeq for Gata1, H3K27ac and H3K36me3.

last: Core Facility

department: Departement of Biomedicine

summary: In vitro differentiation of Nsd1-/- erythroblasts with retroviral expression of wildtype Nsd1, or a catalytically-inactive Nsd1N1918Q SET-domain

overall_design: Add-back experiment with cultured Nsd1-/- erythroblasts rescued with either retroviral expression of wildtype Nsd1, or a catalytically-inactive Nsd1N1918Q SET-domain

first: Katharina

last: Leonards

first: Marwa

last: Almosailleakh

first: Samantha

last: Tauchmann

first: Frederik

last: Bagger

first: Juerg

last: Schwaller


title: Next Generation Sequencing Facilitates Quantitative Analysis of HepG2 cells exploring to the Fluid shear stress

status: Public on Mar 03 2020

city: Chengdu

first: hongchi

last: Yu

state: Sichuan

address: No.24 South Section 1, Yihuan Road

institute: Sichuan University

summary: To investigate the mechanisms underlying Fluid shear stress affecting HepG2 cells motility, we conducted global gene expression profiling of FSS-HepG2 cells compared with static cultured HepG2 cells.

overall_design: two samples, each sample mixed by 3 replicates. HepG2 cells used as control and Fluid shear stress treated HepG2 cells

first: Hongchi

first: Yang

last: Shen


title: Expression data from Limb bud cells

status: Public on Feb 20 2020

city: Suita

first: Yoshifumi

last: Takahata

state: Osaka

department: Dentistry

institute: Osaka University

summary: To identify downstream molecules induced by Bmp2, Limb bud cells were infected with control or Bmp2 adenovirus, and performed microarray analysis.

overall_design: Limb bud cells were prepared from four limbs E12.5day ICR mice. Limb bud cells infected with Venus or Bmp2, and subsequent isolation of total RNA for Affymetrix Mouse Genome 430  2.0 array.


title: Long noncoding RNA and messenger RNA abnormalities in pediatric sepsis

status: Public on Feb 14 2020

city: Suzhou

first: Fang

last: Fang

state: Jiangsu

address: 92 Zhongnan street

institute: Children’s Hospital of Soochow University

type:
Expression profiling by array
Non-coding RNA profiling by array

summary:
Sepsis represents a complex disease with dysregulated inflammatory response and high mortality rate. Long noncoding RNAs (lncRNAs) have been reported to play regulatory roles in a variety of biological processes. However, studies evaluating the function of lncRNAs in pediatric sepsis are scarce, and current knowledge of the role of lncRNAs in pediatric sepsis is still limited.
We explored the expression patterns of both lncRNAs and mRNAs between pediatric sepsis patients and healthy controls based on a comprehensive microarray analysis.

overall_design: Total RNA was extracted using RNAiso (TaKaRa, Dalian, China) from the 10 septic children and 12 controls. Affymetrix Human oelncRNA Array (v1.0) was used to detect the expression of lncRNAs and mRNAs in the septic and control groups.

first: Zhenjiang

last: Bai


title: Expression data of EBV-positive and EBV-negative subclones of gastric adenocarcinoma cell line AGS

status: Public on Oct 14 2019

city: Seoul

first: Suk Kyeong

last: Lee

address: 222, Banpo-daero

country: South Korea

institute: Catholic University of korea

summary: Gastric cancer is one of the most common cancers worldwide. Epstein-Barr virus-associated gastric cancer accounts for approximately 10% of all gastric cancers. EBV expresses its own proteins and miRNAs (BART miRNAs) and regulates host gene expression. In this study, we examined the effect of EBV infection on host mRNA expression. Differential gene expression was analyzed between EBV-negative human gastric cancer cell line AGS and EBV-positive human gastric cancer cell line AGS-EBV.

overall_design: Total RNA was prepared using RNAzol B reagent from five each independent cultures of AGS and AGS-EBV cells.

first: Suk


title: HIF1/2-exerted control over glycolysis but not OxPHOS pathways in human normal and leukemic stem/progenitor cells

status: Public on Feb 04 2020

first: Joost

last: Martens

state: Nederland

department: RIMLS

summary: Hypoxia inducible factors (HIF)1 and 2 are transcription factors which regulate the homeostatic response to low oxygen conditions. Since data related to the importance of HIF1 and 2 in haematopoietic stem and progenitors is conflicting, we investigated the chromatin binding profiles of HIF1 and HIF2 and linked that to transcriptional networks and the cellular metabolic state. Genome-wide ChIP-seq and transcriptome studies revealed that overlapping HIF1- and HIF2-controlled loci were highly enriched for various processes like  including  metabolism, particularly those involved in glucose metabolism, but also for chromatin organization, cellular response to stress and G protein-coupled receptor signaling. ChIP-qPCR validation studies confirmed that glycolysis-related genes - but not genes related to the TCA cycle or glutaminolysis - were controlled by both HIF1 and HIF2 in leukemic cell lines and primary AMLs, while in healthy human CD34+ cells these loci were predominantly controlled by HIF1 but not HIF2. However, and in contrast to our initial hypotheses, CRISPR/Cas9-mediated knockout of HIF signaling did not affect growth, internal metabolite concentrations, glucose consumption or lactate production under hypoxia. These data indicate that, while HIFs exert control over glycolysis but not OxPHOS gene expression in human leukemic cells, this is not critically important for their metabolic state.

overall_design: ChIP-seq analysis of tagged HIF proteins in K562 cells was performed using illumina high-throughput sequencing

first: Albertus

middle: T

last: Wierenga

first: Alan

last: Cunningham

first: Nuria

last: Vilaplana Lopera

first: Ayşegül

last: Erdem

first: Ulrich

last: Günther

last: H.A. Martens

first: Edo

last: Vellenga

first: Jan

last: Schuringa


title: Transcriptomic changes in response to host temperature stress in the pathogen Crypococcus neoformans

status: Public on Sep 26 2019

city: Buffalo

first: John

middle: C.

last: Panepinto

state: NY

address: 955 Main St., Suite 5229

department: Microbiology and Immunology

institute: University at Buffalo SUNY

summary: Using RNA-seq we report the global changes that occur in response to host temperature stress in the pathogen, Crypococcus neoformans, and reveal that mRNA decay plays a critical role in the transcriptomic and translatomic reprogramming necessary for stress adaptation.

overall_design: Total and polysome-associated mRNA profiles of two strains duringoptimal conditions and one hour following host temperature stress were generated by RNA-seq.

middle: C

first: Amanda

middle: L

last: Bloom

first: Jonathan

last: Bard


title: Lymphoma angiogenesis is orchestrated by noncanonical signaling pathways

status: Public on Sep 01 2019

city: Münster

first: Michael

last: Grau

state: Nordrhein-Westfalen

address: Albert-Schweitzer-Campus 1

department: Faculty of Medicine

institute: University of Münster

summary: Angiogenesis is a hallmark of the tumor microenvironment that correlates with the prognosis of aggressive B cell lymphoma. Targeting established angiocrine pathways in lymphoma failed to improve treatment efficacy. Here, we model Myc-driven B cell lymphoma-induced angiogenesis. Few lymphoma cells are sufficient to activate the angiogenic switch in lymph nodes. The unique morphology of dense microvessels emerges without tip cell guidance and rests on blood endothelial cell (BEC) proliferation and aberrant sprouting. The transcriptional response of BECs is inflammation independent. Conventional HIF1alpha or Notch signaling routes prevalent in solid tumors are not involved. Instead, a non-conventional hypersprouting morphology is orchestrated by lymphoma-provided VEGF-C and lymphotoxin (LT). Interference with VEGFR-3/VEGF-C and LT/LTbR loops abrogated angiogenesis, thus revealing targets to block lymphomagenesis.

overall_design: Gene expression in lymph node stromal cells (BEC, LEC, FRC, DN) were compared with each other and tumor versus naïve. For tumor and naïve, each cell type was measured in three biological replicates with two technical replicates each (2*4*3*2=48 samples).

first: Armin

last: Rehm

first: Georg

last: Lenz


title: Comparative expression analysis of the Arabidopsis strigolactone (SL)-receptor mutant, d14-1, and wild type (WT) plants (Col-0) under dehydration conditions.

status: Public on Jan 18 2020

city: Hanoi

first: Kien

middle: Huu

last: Nguyen

state: Bac Tuliem

address: Pham Van Dong str., Bac Tuliem, Hanoi, Vietnam

department: Genetic Engineering Department

country: Viet Nam

institute: Agricultural Genetics Institute

summary: To understand the role of SL-signaling components in water stress response, we have carried out comparative expression analysis of the SL-receptor d14-1 mutant and WT plants under dehydration and well-watered (control) conditions. Aligent’s whole Arabidopsis Gene Expression Microarray (G2519F-021169, V4, 4x44K) was used.

overall_design: Two-week-old WT and d14-1 mutant plants were transferred from GM plates to soil and grown for 10 additional day. The aerial parts of 24-d-old plants were detached and exposed to dehydration on KimTowel papers for 0 (well-watered, control), 2 and 4 h. All rosette leaves of independent 24-d-old plants were collected. Total RNA was prepared and used for the microarray hybridization. Four independent biological replicates were used for each plant sample.

first: Weiqiang

last: Li

first: Maho

last: Tanaka

first: Motoaki

last: Seki

first: Lam-Son

middle: P

last: Tran


title: Multiple sclerosis cortical normal-appearing grey matter and grey matter lesions

status: Public on Jan 13 2020

first: DBM Bioinformatics

last: Core Facility

state: BS

summary: Multiple sclerosis (MS) is a chronic inflammatory demyelinating disease of the brain. Among characteristics of MS pathology are cortical grey matter abnormalities, which have been linked to clinical signs such as cognitive impairment. To understand MS cortical grey matter lesion pathogenesis, we performed differential gene expression analysis of MS cortical normal-appearing grey matter (NAGM) and grey matter lesions. HLA-DRB1 is the transcript with highest expression in MS NAGM with a bimodal distribution among the examined cases. Genotyping revealed that every case with the MS-associated HLA-DR15 haplotype also shows high HLA-DRB1 expression. Quantitative immunohistochemical analysis confirmed the higher expression of HLA-DRB1 in HLA-DRB1*15:01 cases at the protein level. Analysis of grey matter lesion size revealed a significant increase of cortical lesion size in cases with high HLA-DRB1 expression. Our data indicate that increased HLA-DRB1 expression in the brain of MS patients may be an important factor in how the HLA-DR15 haplotype contributes to MS risk in the target organ.

overall_design: MS- and control tissue samples were provided by the UK Multiple Sclerosis Tissue Bank (UK Multicentre Research Ethics Committee, MREC/02/2/39). In total, 41 normal-appearing grey matter tissue samples from 20 MS cases and 37 cortical grey matter lesion tissue samples from 18 MS cases were used for the gene expression analysis between multiple sclerosis grey matter lesion and normal-appearing grey matter.

first: L

last: Enz

first: T

last: Zeis

first: F

last: Geier

first: D

last: Schmid

first: G

last: Steiner

first: U

last: Certa

first: N

last: Schaeren-Wiemers


title: Expression data from Il-27 stimulated normal human epidermal keratinocytes (NHEK) and THP-1 cells

status: Public on Jan 08 2020

city: Chapel Hill

first: David

last: Corcoran

state: NC

address: 125 Mason Farm Rd

department: Genetics

institute: University of North Carolina at Chapel Hill

summary: IL-27 plays a pivotal role in regulating complex immune responses. To evaluate the role of IL-27 in modulation in the expression of cellular and innate immunity-asscoiated genes in human epidermal keratinocytes (primary cells) and the monocytic THP-1 cell line (pre-treated with PMA) were stimulated with IL-27 and genome-wide expression of these cells were investigated utilizing microarray assay.

overall_design: Human epidermal keratinocytes (primary cells) and the monocytic THP-1 cell line (pre-treated with PMA) were stimulated with IL-27 (100ng/ml); Stimulated) or vehicle control (Non-stimulated) and genome-wide expression of these cells were investigated utilizing U133 Plus microarray assay.

first: Amanda

last: MacLeod


title: Defining the microglial transcriptome in the rat subventricular zone (SVZ) after neonatal hypoxia-ischemia (HI).

summary: Purpose: Recent findings indicate a regulatory role of microglia on neurogenesis in the SVZ in health and disease. Microglia in the early postnatal SVZ are not fully maturated and may react differently than adult microglia to injury. We sought to investigate the impact of cortico-striatal neonatal HI injury on the microglial phenotype in the early postnatal SVZ. Results: In comparison to sham SVZ microglia, HI SVZ microglia upregulate both pro- and anti-inflammatory genes as well as neurotrophic genes. HI SVZ microglia do not adopt a M1 or M2 polarization state, but instead share commonly expressed genes with microglia in rodent models of neurodegenerative diseases.

overall_design: Total RNA was extracted from anti-CD11b magnetic bead isolated microglia from the dorsolateral SVZ or M2 supplementary motor cortex (CX) of individual rats: Postnatal day (P) 7 Sprague-Dawley rats were subjected to sham surgery (exposure of the right [ipsilateral] common carotid artery) or HI surgery (temporary occlusion of the ipsilateral common carotid artery and exposure to hypoxia).  The anterior dorsolateral SVZ (ipsilateral in HI animals, ipsi- and contralateral in sham animals) and the contralateral CX were microdissected, CD11b+ cells isolated and total RNA extracted at P10 or P20, respectively.

first: Urs

last: Fisch

first: Florian

first: Raphael

last: Guzman


title: Genome-wide profiling of nucleosomes (MNase-seq), total H3, H3K4me2, H3K4me3 and H3K36me3 (native ChIP-seq) in wild-type, fpa mutant and bdrs triple mutant

status: Public on Aug 08 2019

city: Villenave d'Ornon

first: Pascal

middle: GP

last: Martin

address: 71 avenue Edouard Bourlaux

department: UMR1332 BFP

country: France

institute: INRAE

summary: We used an MNase digestion of chromatin from Arabidopsis seedlings, combined or not with ChIP (native ChIP), to analyze by high-throughput sequencing the genome-wide profiles of nucleosomes (MNase-seq), and of total H3, H3K4me2, H3K4me3 and H3K36me3 (native ChIPs) in wild-type (Col-0), fpa mutant (fpa/AT2G43410, line fpa-7) and a triple mutant of all three BDR proteins (bdrs: cross of bdr1/AT5G25520 mutant SALK_142108C, bdr2/AT5G11430 mutant CS852350 and bdr3/AT2G25640 mutant SALK_059905). We found that BDR proteins occupy regions of low nucleosome density. We also observed that genes upregulated in bdrs triple mutant display high levels of RNA polymerase II on their gene bodies but low levels of H3K4me3 and H3K36me3 in wild-type seedlings. For genes with the highest levels of BDR occupancy in wild-type, increased mRNA expression in bdrs mutant is associated with reduced RNA polymerase II density profile and increased H3K4me3 and H3K36me3 levels.

overall_design: Genome-wide profiles using native (non crosslinked) chromatin from 8-day old seedlings of nucleosomes (MNase-seq), total H3, H3K4me2, H3K4me3 and H3K36me3 (native ChIP) in wild-type, fpa single mutant (fpa-7) or bdrs triple mutant were generated by deep sequencing on an Illumina NextSeq500. MNase-seq corresponds to the input chromatin sample used for the immunoprecipitation.

first: Scott

middle: D

last: Michaels

first: Xuhong

last: Yu

first: Jie

last: Huang

first: James

middle: B

last: Ford


title: The Branched-Chain Amino Acid Transporter CD98 Heavy Chain Facilitates the Development of Colonic Macrophages Associated with Decreased Apoptosis in Macrophage Progenitors

status: Public on Jan 21 2020

first: DBM Bioinformatics

last: Core Facility

summary: We performed a single-cell transcriptome analysis of colon monocytes and macrophages from corn oil treated CD98ΔCX3CR1 mice and tamoxifen induced conditional Cd98 KO (CD98ΔCX3CR1) mice.

overall_design: Lamina propria cells positive for Cd11b and positive for Ccr2 or Cd64 were sorted from 4 control (corn oil) mice and 4 tamoxifen induced Cd98 KO mice and used for single cell RNA Seq (10x genomics platform)

first: Philipp

last: Wuggenig

first: Jan

last: Niess

first: Julien

last: Roux


title: miR-19b-3p Overexpression in Human Skeletal Muscle Cells

city: Stockholm

first: Anna

last: Krook

address: von Eulers väg 4a

country: Sweden

institute: Karolinska Institutet

summary: The object of this data set was to indentify genes altered by miR-19b-3p in differentiated human skeletal muscle myotubes.

overall_design: We transfected human skeletal muscle cells as differentiated myotubes either with a miR-19b-3p mimic (miR) or a negative control mimic (NC)  (miR™ miRNA Precursors; Thermo Fisher Scientific). Cells were transfected twice with a gap of 48 hours between transfections and RNA was extracted by TRIzol 48 hours after the second transfection. In total there are 8 samples of human skeletal muscle cells; 2 samples (NC and miR; paired analysis) from 4 different human donors.


title: Single cell RNA-sequencing of cardiac CD45+ populations in mouse with transverse aortic constriction (TAC)

status: Public on Dec 30 2019

city: Guangzhou

first: Lu

last: Lu

address: No.12,Airport Road,Baiyun District

institute: Guangzhou University of Chinese Medicine

summary: It is already well known that the immune cells called macrophages are involved in the mechanisms of heart failure (HF). Macrophages are divised into several subtypes based on behavior.Some subsets are highly inflammatory, while some support tissue repair. Recent studies have suggested that the classical M1/M2 classification is not suitable for some pathological processes of the heart. Single cell sequencing (scSeq) is an ideal tool to clarify the macrophage heterogeneity in HF. It provided a higher resolution of cellular differences and a better understanding  of  individual cell function. In this study, we aimed to identify a macrophage subset that linked with heart failure, and furtherly screen the target and investigate the mechanism.

overall_design: CD45+ cells from heart of mice with/without TAC (6 per group) were sorted and the mRNA profiles of single cells were investagted by 10x Genomics technology

first: Ni

last: Shi-Hao


title: The FAK-Inhibitor BI 853520 exerts anti-tumor effects in breast cancer

status: Public on Jul 19 2019

city: Basel

institute: University of Basel

summary: In order to delineate the molecular mechanisms leading to the therapeutic effect of BI 853520 on primary tumor growth, mice harboring 4T1 primary tumors were treated for five days with BI 853520, and RNA extracted from total tumors was subjected to next generation sequencing. Only primary tumors with sufficient RNA quality were included into further analysis (Suppl. Fig. 2A). Gene expression correlation analysis displayed a clear separation of transcriptomic profiles derived from primary tumors of mice treated with BI 853520 or vehicle (Suppl. Fig. 2B). Comparative gene expression analysis of primary tumors of mice treated with BI 853520 versus vehicle control revealed 1293 upregulated and 475 downregulated genes (cutoffs: p-value ≤ 0.05, fold change +/- 1.5). Functional enrichment analysis for biological processes and signaling pathways indicated that the regulation of epithelial cell proliferation, positive regulation of cell cycle/cell proliferation/cell division and regulation of cell proliferation/cell division/cell growth were enriched in genes downregulated by BI 853520 treatment (Fig. 3A). In line with this finding, gene set enrichment analysis confirmed a significant reduction in the relative expression of genes important for cell cycle and positive regulation of mitotic cell cycle (including cyclin-dependent kinase 1 and 4; Cdk1: log2 fold-change= -0.4519, FDR= 4.24e-03; Cdk4: log2 fold-change= -0.3072, FDR= 0.003718), while the negative regulation of cell proliferation was increased following BI 853520 treatment (Fig. 3C; Suppl. Fig. 2C).

overall_design: BI 853520 was administered from day 15 post injection for five consecutive days. RNA was isolated from snap-frozen 4T1 primary tumor pieces and applied to next generation sequencing.

first: Ruben

last: Bill

first: Ravi

last: Kalathur

first: Robert

last: Ivanek

first: Gerhard

last: Christofori


title: Dissecting polymerase pausing with TV-PRO-seq

status: Public on Aug 01 2019

city: Coventry

last: Zhang

address: School of Life Sciences, Gibbet Hill Campus, The University of Warwick

department: School of Life Sciences

country: United Kingdom

institute: University of Warwick

summary: Transcription of many genes in metazoans is subject to polymerase pausing, which corresponds to the transient arrest of transcriptionally engaged polymerase. It occurs mainly at promoter proximal regions and is not well understood. In particular, a genome-wide measurement of pausing times at high resolution has been lacking. This is because relevant experimental techniques are mostly based on average polymerase occupancies across many cells which cannot discriminate between few slow polymerases and many quick polymerases at a position, since the data corresponds to the average of many cells. We present here an extension of the PRO-seq assay, which we termed time variant PRO-seq (TV-PRO-seq)based on a detailed analysis of the logics underlying PRO-seq, that achieves this goal.

overall_design: The main TV-PRO-seq experiment consisted of 8 independent PRO-seq samples : biological duplicates of the 4 run-on times 30sec, 2min, 8min and 32min. The TV-PRO-seq have been  performed in 2 human cell lines KBM7 and HEK293. Two triptolide treatment sample have been taken in KBM7 cells for 3min and 6min run-on, DMSO treatment have been use for control for the same run-o time.

first: Massimo

last: Cavallaro

first: Daniel

last: Hebenstreit


title: Assay for Transposase-Accessible Chromatin using sequencing of spleen memory CD4+ T cells

status: Public on Dec 04 2019

address: Hebelstrasse 20

summary: We performed a ATAC seq analysis of 2 biological independent splenic samples from pooled mice sorted for lcmv-specific memory CD4 T cells and 2 technical replicates from one mouse sorted for naive CD4 T cells .

overall_design: Cells negative for dump and positive for CD4, CD44 and gp66 and either Ly6C+ PSGL-1+ (Th1) Ly6C-PSGL-1- (TFH) or dump- CD4+ CD44- CD62L+ for naive CD4 T cells were sorted for each replicate, and used for ATAC Seq

first: Marco

last: Kuenzli

first: David

last: Schreiner

first: Florian

last: Geier

first: Carolyn

last: King


title: The interplay between IL-15, gluten and HLA-DQ8 drives the development of coeliac disease in mice

status: Public on Jul 26 2019

city: Chicago

first: Luis

last: Barreiro

address: 900 E 57th Street

country: USA

institute: University of Chicago

summary: Coeliac disease (CeD) is a complex, polygenic inflammatory enteropathy with autoimmune features caused by exposure to dietary gluten that occurs in a subset of genetically susceptible HLA-DQ8 and HLA-DQ2 individuals. Attempts to develop a pathophysiologically relevant animal model that develops villous atrophy (VA) have failed. The need to develop non-dietary treatments for this common disorder is now widely recognized, but it is hampered by the lack of a preclinical model. Furthermore, while human studies have led to major advances in our understanding of CeD pathogenesis, direct demonstration of the respective roles of disease-predisposing HLA molecules, and adaptive and innate immunity in the development of tissue damage is missing. To address these unmet needs, we engineered a mouse model that reproduces the dual overexpression of IL-15 in the gut epithelium and the lamina propria (Lp) characteristic of active CeD, expresses the predisposing HLA-DQ8 molecule, and develops VA upon gluten ingestion. We show that overexpression of IL-15 in both the epithelium and Lp is required for development of VA, demonstrating the location-dependent central role of IL-15 in CeD pathogenesis. Furthermore, our study reveals the critical role played by both CD4+ and cytotoxic CD8+ T cells in VA development. Finally, it establishes that HLA-DQ8 is central for tissue destruction, but dispensable for loss of oral tolerance to gluten. This mouse model, by reflecting the complex interplay between gluten, genetics and the IL-15-driven tissue inflammation found in CeD, represents a powerful preclinical model to test new therapeutics and study disease pathogenesis.

overall_design: We collected RNA-sequencing data from duodenal biopsies obtained from 51 CeD patients and 45 healthy controls.

first: Bana

last: Jabri


title: RNA-seq analysis of transcriptome reprofiling triggered by different pattern-recognition receptor types

status: Public on Jun 21 2019

city: Oxford

first: Maricris

last: Zaidem

state: Oxfordshire

address: South Parks Rd

department: Department of Biology

institute: University of Oxford

summary: Plant cell surface receptors sense microbial pathogens by recognizing microbial structures called pathogen or microbe-associated molecular patterns (PAMPs/MAMPs). There are two major types of plant pattern recognition receptors: 1. Leucine-rich repeat receptor proteins (LRR-RP) and LRR receptor kinases (LRR-RK) and 2. Plant receptor proteins and receptor kinases carrying ectopic lysin motifs (LysM-RP and LysM-RK). In this study, Arabidopsis thaliana responses to three different MAMPs, flg22, nlp20, chitin (C6), via their corresponding receptor types, FLS2 (LRR-RK), RLP23 (LRR-RP), CERK1 (LysM-RK) were compared. Our RNA-seq results indicate that a core set of defense-related genes can be activated through perception of different MAMPs. However, there are also notable differences in the transcriptional changes in response to the various elicitors; flg22 causes broader transcriptome changes than nlp20 and C6, and C6 does not cause late transcriptome changes.

overall_design: Arabodopsis seedings were treated with water, flg22, nlp20, or C6 and collected after 1h, 6h and 24h. One sample before treatment was also collected. 4 biological repecates were performed.

first: Wei-Lin

last: Wan

first: Thorsten

last: Nuernberger


title: TORC1 is required for the entry of yeast gametes into the mitotic cell cycle

status: Public on Dec 31 2019

city: Singapore

first: Prakash

last: Arumugam

state: Singapore

address: Biomedical sciences Institute Bioinformatics Institute, A*STAR 30 Biopolis Street, #07-01, Matrix

department: Translational division

institute: BII

summary:
Purpose:To identify the targets of TORC1 during spore germination in budding yeast
Results:We obtained the transcriptomes of germinating spores in the presence and absence of rapamycin with and  average Read Count = 14,009,863 and an Average Overall alignment: 95.23%. Differentialy expressed genes were identified by comparing the spore germination at various time points in the presence and absence of Rapamycin.
Conclusions: Our transcriptomic analyses has revealed a role for TORC1 in regulating the glucose response genes

overall_design: Methods: mRNA profiles of germinating spores in the presence and absence of rapamycin were generated by deep sequencing, in triplicate, using Illumina GAIIx. The sequence reads that passed quality filters were analyzed at the transcript  level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks. qRT–PCR validation was performed using  SYBR Green assays

first: Mohammad

last: Alfatah

first: Vidhya

last: Gomathi Krishnan

first: Jin

last: Wong

first: Kiat

last: Kong

first: Shawn

last: Hoon


title: Long-lived T follicular helper cells retain plasticity and help sustain humoral immunity

first: DBM Bioinformatics

last: Core Facility

country: Switzerland

summary: This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: Social history and exposure to pathogen signals modulate social status effects on gene regulation in rhesus macaques

status: Public on Aug 22 2019

summary: Social experiences are an important predictor of disease susceptibility and survival in humans and other social mammals. Chronic social stress is thought to generate a pro-inflammatory state characterized by elevated antibacterial defenses and reduced investment in antiviral defense. Here, we manipulated long-term social status in female rhesus macaques to show that social subordination alters the gene expression response to ex vivo bacterial and viral challenge. As predicted by current models, bacterial lipopolysaccharide polarizes the immune response such that low status corresponds to higher expression of genes in NF-κB dependent pro-inflammatory pathways and lower expression of genes involved in the antiviral response and type I interferon (IFN) signaling (see Snyder-Mackler et al. Science, 2016 doi:10.1126/science.aah3580 and GSE83304). Here we show that, counter to predictions, low status drives more exaggerated expression of both NF-κB and IFN-associated genes after cells are exposed to the viral mimic Gardiquimod. Status-driven gene expression patterns are not only linked to social status at the time of sampling, but also to social history (i.e., past social status), especially in unstimulated cells. However, for a subset of genes, we observed interaction effects in which females who fell in rank were more strongly affected by current social status than those who climbed the social hierarchy. Together, our results indicate that the effects of social status on immune cell gene expression depend on pathogen exposure, pathogen type, and social history – in support of social experience-mediated biological embedding in adulthood, even in the conventionally memory-less innate immune system.

overall_design: mRNA sequencing of Gardiquimod treated whole blood from female rhesus macaques

first: Joaquín

last: Sanz

first: Jenny

last: Tung


title: Genome-wide differential expression profiling of ovarian circRNAs associated with litter size in pigs

status: Public on Sep 05 2019

city: Ynagling

first: Shiduo

last: Sun

address: Xinong Rd #22

institute: Northwest A&F University

summary: In this study, porcine ovaries with smaller or larger litter size (SLS or LLS) were subjected to high-throughput RNA-sequencing. In total, 38,722 circRNAs were identified, of which 1,291 circRNAs were commonly expressed in all samples. There were 56 circRNAs significantly down-regulated and 54 circRNAs up-regulated in LLS pig. Besides, 411 miRNAs were identified, and of these 17 were significantly down-regulated and 16 miRNAs were up-regulated when comparing sows with LLS and SLS, respectively. In addition, we identified a total of 3,556 lncRNA candidates, of which 96 lncRNAs were up-regulated and 206 lncRNAs were down-regulated when comparing LLS to SLS. 16,428 genes were detected, and 2,392 unigenes were significantly differently expressed at the LLS and SLS ovarian samples. In addition, a competitive endogenous RNA (ceRNA) network was constructed. Our study indicates that non-coding RNAs may play roles in modulating porcine litter size.

overall_design: For RNA-seq, 3 ovaries were sampled from each group small and large litter size (8.48±0.53 piglets/litter in small litter size, and 16.19±0.43 piglets/litter in large litter size).

first: Gaoxiao

last: Xu

first: Huifang

last: Zhang

first: Xiao

last: Li

first: Jianhong

last: Hu

first: Gongshe

last: Yang


title: Bulk RNA-sequencing of spleenic LCMV-specific memory TFH cells treated with aICOSL.

status: Public on Dec 05 2019

summary: We performed RNA-seq analysis of splenic samples from 8 individual mice sorted for LCMV-specific memory follicular B helper T cells (TFH) with or without aICOSL treatment (4 samples per group).

overall_design: Cells negative for dump and positive for CD4, CD44 and gp66 and Ly6C-PSGL-1- (TFH) were sorted for each sample.

first: Marco

last: Kuenzli

first: David

last: Schreiner

first: Julien

last: Roux

first: Carolyn

last: King


title: RNA-seq analysis of transcriptomic changes in bone marrow LSK cells in WT, G12D, Ezh2-KO and G12D with Ezh2-KO (G12D_Ezh2-KO) mice [RNA-seq]

status: Public on Jun 17 2019

city: Memphis

first: Jian

state: Tennessee

address: 262 Danny Thomas Place, MS 345

department: Pathology

institute: St. Jude Children's Research Hospital

summary: Epigenetic gene regulation and metabolism are highly intertwined, yet little is known whether and how altered epigenetics influences cellular metabolism in cancer progression. Here we show that EZH2 and NRasG12D mutations cooperatively induce progression of myeloproliferative neoplasms to fully penetrant, transplantable and lethal myeloid leukemias in mouse. EZH1, an EZH2 homolog, is indispensable for EZH2-deficient leukemia-initiating cells (LICs) and constitutes an epigenetic vulnerability. BCAT1, the first enzyme catalyzing transamination of branched-chain amino acids (BCAAs), is repressed by EZH2 in normal hematopoiesis and aberrantly activated in EZH2-deficient myeloid neoplasms in mouse and human. Enhanced BCAT1 promotes BCAA production in LICs ex vivo and in vivo, resulting in activated mTOR signaling. Genetic and pharmacological inhibition of BCAT1 selectively impairs EZH2-deficient LICs and constitutes a metabolic vulnerability. These findings establish an example how epigenetic alterations modify metabolic adaptation in myeloid transformation and provide a rationale for targeting the epigenetic and metabolic liabilities of cancer-initiating cells.

overall_design: RNA-seq was performed to determine the transcriptomic changes in FACS-sorted LSK cells from WT, G12D, Ezh2-KO and G12D with Ezh2-KO (G12D_Ezh2-KO) mice

first: Zhimin

last: Gu

first: Yuxuan

last: Liu


title: Molecular profiling predicts meningioma recurrence and reveals loss of DREAM complex repression in aggressive tumors

status: Public on Nov 13 2019

city: Houston

first: Tiemo

last: Klisch

address: 1250 Moursund Street, N1370.08

department: Department of Molecular and Human Genetics

institute: Baylor College of Medicine

summary: Meningiomas account for roughly one-third of all primary brain tumors. Although typically benign, about 20% of meningiomas are aggressive, and despite the rigor of the current histopathological classification system, there  remains considerable uncertainty in predicting tumor behavior. Here we analyzed 160 tumors from all three WHO grades (I-III) using clinical, gene expression and sequencing data. Unsupervised clustering analysis identified three molecular groups that reliably predicted clinical severity. These groups did not directly correlate with the WHO grading system, which would classify more than half of the tumors in the most aggressive molecular group as benign. Transcriptional and biochemical analyses revealed that aggressive meningiomas involve loss of the repressor function of the DREAM complex, resulting in cell cycle activation, and only tumors in this group tend to recur after full resection. These findings should improve our ability to predict recurrence and develop targeted treatments for these clinically challenging tumors.

overall_design: Discovery set: 97 tumors, Validation set: 48 tumors, Recurrence set: 15 tumors.

first: Akash

last: Patel

first: Ying

last: Wan

first: Huda

middle: Y

last: Zoghbi


title: Transcriptomic profiling of MDA-MB-468 cells treated with TNFɑ [40 ng/ml] ± Apigenin [40 μM].

status: Public on Jul 09 2019

city: Tallahassee

first: Elizabeth

middle: A

last: Mazzio

address: 1515 MLK Blvd

department: College of Pharmacy & Pharmaceutical Science

institute: Florida Agricultural & Mechanical University

summary: Gene expression data from MDA-MB-468 cells grown under variable experimental treatment

overall_design: The effects of TNFɑ [40 ng/ml] ± Apigenin [40 μM] were evaluated in MDA-MB-468 cells using GeneChip™ Human Gene 2.1 ST Arrays by Affymetrix Inc assessing for mRNAs and long intergenic non-coding RNA transcripts.

last: Bauer

first: Karam

last: Soliman


title: scRNA-seq reveals development of a broad spectrum of cell types in human iPSC derived hepatic organoids (HOs) and defines biomarkers in iPSC to liver lineage differentiation stages

status: Public on Oct 26 2019

city: PALO ALTO

first: YUAN

last: GUAN

state: CA

address: 1701 Page Mill Road

institute: Stanford University

summary: At each differentiation stage, HO cultures contain different types of cells, and sub-populations of each cell type can be in various stages of differentiation; which makes it very difficult to identify critical transcriptional changes through analyses performed on the bulk population. To deal with the cellular complexity within dynamically changing organoid cultures at different developmental stages, single cell RNA sequencing (scRNA-Seq) can be used to simultaneously analyze global changes in the transcriptome of many individual cells.

overall_design: To characterize the dynamic changes that occur as a control iPSC line (C1, C2 and C3) differentiates into an organoid, scRNA-Seq was performed on the iPSC, day 9 hepatoblasts (HB), day 21 HO (phLO) and secondary organoid in growth media (GM) and differentiation media (DM) cultures; and scRNA-Seq was also performed on primary human hepatocytes (PHHs) for comparison purposes. Samples that passed the following criteria were retained for subsequent analysis: 1) the total number of reads should be at least 105, 2) the number of genes detected in the sample should >3000, and 3) <50% of the reads were mapped to the 37 mitochondrial genes. In the 1st sample set, 114 samples passed this QC step (25 iPSC, 25 HB, 50 HO and 14 PHH samples). In the 2nd sample set, 310 samples passed this QC step (16 iPSC, 124 HB and 170 HO samples). Therefore, 424 samples were subsequently analyzed (65, 71, 185 and 89 samples for A1, A2, C1 and C2, respectively, and 14 PHH samples).

first: Yuan

last: Guan

first: Ming

last: Zheng